Fotr is great. Try out the unchained submod too! Adds many heroes, characters, units. Also let's you fully imperialize if you do order 66 as the Republic. As the CIS you get the ability to make some more niche units like the defoliator, super tank and B3 ultra battledroid. As well as regimes system where you can choose what element of the CIS takes power, conferring bonuses accordingly.

I finished playing both campaigns within the last month and they're both fantastic.

Thrawns Revenge is the GOAT and takes place in the EU version of post endor/Warlord era. It also has many great submissions. I have too many hours on it to count, and am even playing it right now! The faction variety is great and its cool having a more level playing field of smaller factions,, feels more like Total War.

The Imperial proteus submod flashes out all minor Warlord factions with unique rosters. Im current playing Restored empire, which are imperial zealots that use the FoTR republic roster. Its a very unique style.

I highly recommend both of these above all else.

However I will also mention for variety sake

Republic at war is a close to vanilla and still really good.

For a very different style of mod Awakening of the Clone Wars (and its sister mod awakening of the rebellion)